Strain identifier

BacDive ID: 1884

Type strain: Yes

Species: Brucella tritici

Strain Designation: SCII24

Strain history: Lebuhn M. DSV-DEVM and GSF - NationalResearch Center forEnvironment and Health

NCBI tax ID(s): 94626 (species)

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General

@ref: 5003

BacDive-ID: 1884

DSM-Number: 13340

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Brucella tritici SCII24 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere of wheat.

NCBI tax id

  • NCBI tax id: 94626
  • Matching level: species

strain history

@refhistory
5003<- M. Lebuhn; SCII24
67772Lebuhn M. DSV-DEVM and GSF - NationalResearch Center forEnvironment and Health

doi: 10.13145/bacdive1884.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Brucellaceae
  • genus: Brucella
  • species: Brucella tritici
  • full scientific name: Brucella tritici (Lebuhn et al. 2000) Hördt et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Ochrobactrum tritici

@ref: 5003

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Brucellaceae

genus: Brucella

species: Brucella tritici

full scientific name: Brucella tritici (Lebuhn et al. 2000) Hördt et al. 2020

strain designation: SCII24

type strain: yes

Morphology

cell morphology

  • @ref: 23335
  • gram stain: negative
  • cell length: 0.6-1.4 µm
  • cell width: 0.4-0.6 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: peritrichous

colony morphology

  • @ref: 23335
  • colony color: opaque
  • medium used: NA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5003NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
23335Nutrient agar (NA)yes
33780MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)

culture temp

@refgrowthtypetemperaturerange
5003positivegrowth30mesophilic
23335positivegrowth4-40
23335positiveoptimum30mesophilic
33780positivegrowth30mesophilic
57511positivegrowth30mesophilic
67772positiveminimum4psychrophilic
67772positiveoptimum30mesophilic
67772positivemaximum40thermophilic

culture pH

@refabilitytypepHPH range
23335positivegrowth3.0-9.0alkaliphile
23335positiveoptimum6.0-7.0
67772positiveoptimum6.0-7.0
67772positivemaximum9.0
67772positiveminimum3.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23335aerobe
57511aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2333517521(-)-quinic acid-assimilation
23335645522-hydroxybutyrate-assimilation
2333522599arabinose-assimilation
2333517057cellobiose-assimilation
2333528066gentiobiose-assimilation
2333517754glycerol-assimilation
2333515792malonate-assimilation
2333537684mannose-assimilation
2333528053melibiose-assimilation
2333517151xylitol-assimilation
2333515963ribitol+assimilation
2333517784D-glucosaminic acid+assimilation
2333516551D-trehalose+assimilation
2333524265gluconate+assimilation
2333517306maltose+assimilation
2333541865sebacic acid+assimilation
2333516947citrate+/-assimilation
2333517126DL-carnitine+/-assimilation
2333514336glycerol 1-phosphate+/-assimilation
2333516704uridine+/-assimilation
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantis intermediateis sensitive
2333517698chloramphenicolyesyes
2333537943colistinyesyes
2333537943colistinyesyes
233358309polymyxin byesyes

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
23335catalase+1.11.1.6
23335cytochrome oxidase1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
5003+---+---++++/-++++-++-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
5003rhizosphere of wheatFranceFRAEurope
23335rhizoplane of wheat (Triticum aestivum)
57511Wheat rhizoplaneFranceFRAEurope1997Grignon
67772Wheat rhizoplaneFranceFRAEuropeAuvergne-Rhône-Alpes, Grignon

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Plant#Rhizoplane
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2226.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_45;97_1426;98_1736;99_2226&stattab=map
  • Last taxonomy: Ochrobactrum
  • 16S sequence: AB681865
  • Sequence Identity:
  • Total samples: 2394
  • soil counts: 432
  • aquatic counts: 339
  • animal counts: 1469
  • plant counts: 154

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
50031Risk group (German classification)
677721

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Ochrobactrum tritici gene for 16S rRNA, partial sequence, strain: NBRC 102585AB6818651408ena94626
20218Ochrobactrum tritici 16S rRNA gene (partial), 23S rRNA gene (partial), tRNA-Ile gene, tRNA-Ala gene and ITS1, type strain SCII24, allele BAJ867329964ena94626
20218Ochrobactrum tritici 16S rRNA gene (partial), 23S rRNA gene (partial), tRNA-Ile gene, tRNA-Ala gene and ITS1, type strain SCII24, allele AAJ867330934ena94626
23335Ochrobactrum tritici partial 16S rRNA gene, strain SCII24AJ2425841398nuccore94626

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brucella tritici DSM 13340GCA_012395245contigncbi94626
66792Ochrobactrum tritici strain DSM 1334094626.11wgspatric94626
66792Ochrobactrum tritici strain LMG 1895794626.9wgspatric94626
67772Brucella tritici LMG 18957GCA_008932295contigncbi94626

GC content

  • @ref: 23335
  • GC-content: 59.00
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes83.455yes
flagellatedno87.191no
gram-positiveno98.364no
anaerobicno97.425no
halophileno92.049no
spore-formingno96.741no
thermophileno98.905no
glucose-utilyes92.639yes
aerobicyes91.457yes
glucose-fermentno90.876yes

External links

@ref: 5003

culture collection no.: DSM 13340, NBRC 102585, CCUG 47104, LMG 18957, UCCCB44

straininfo link

  • @ref: 71528
  • straininfo: 13104

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11155998Taxonomic characterization of Ochrobactrum sp. isolates from soil samples and wheat roots, and description of Ochrobactrum tritici sp. nov. and Ochrobactrum grignonense sp. nov.Lebuhn M, Achouak W, Schloter M, Berge O, Meier H, Barakat M, Hartmann A, Heulin TInt J Syst Evol Microbiol10.1099/00207713-50-6-22072000Alphaproteobacteria/*classification/genetics/immunology/isolation & purification/metabolism, Antibodies, Bacterial/immunology, Antibodies, Monoclonal/immunology, Bacterial Typing Techniques, DNA, Ribosomal/analysis, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Roots/*microbiology, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Triticum/*microbiologyGenetics
Phylogeny17392207Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in Spain.Zurdo-Pineiro JL, Rivas R, Trujillo ME, Vizcaino N, Carrasco JA, Chamber M, Palomares A, Mateos PF, Martinez-Molina E, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.64613-02007Base Composition, Cytisus/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Ochrobactrum/*classification/genetics/isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, SpainGenetics
Genetics18554386Sequencing and expression of two arsenic resistance operons with different functions in the highly arsenic-resistant strain Ochrobactrum tritici SCII24T.Branco R, Chung AP, Morais PVBMC Microbiol10.1186/1471-2180-8-952008Amino Acid Sequence, Antimony, Arsenicals/*pharmacology, Bacterial Proteins/chemistry/genetics/metabolism, Base Sequence, Blotting, Southern, *Drug Resistance, Bacterial, Escherichia coli/genetics/metabolism, *Gene Expression Regulation, Bacterial, Genome, Bacterial, Molecular Sequence Data, Ochrobactrum/classification/*drug effects/*genetics/metabolism, *Operon, Sequence Alignment, Sequence AnalysisMetabolism
Metabolism19525272Identification of an aox system that requires cytochrome c in the highly arsenic-resistant bacterium Ochrobactrum tritici SCII24.Branco R, Francisco R, Chung AP, Morais PVAppl Environ Microbiol10.1128/AEM.02798-082009Anti-Bacterial Agents/metabolism/*pharmacology, Arsenates/metabolism/pharmacology, Arsenic/metabolism/*pharmacology, Arsenites/metabolism/pharmacology, Bacterial Proteins/genetics/metabolism, Biotransformation, Cytochromes c/*metabolism, DNA, Bacterial/chemistry/genetics, *Drug Resistance, Bacterial, Molecular Sequence Data, Multigene Family, Ochrobactrum/*drug effects/genetics/*metabolism, Operon, Oxidation-Reduction, Oxidoreductases/genetics/metabolism, Sequence Analysis, DNA, Sulfurtransferases/genetics/metabolismGenetics
Metabolism26132104Hyper Accumulation of Arsenic in Mutants of Ochrobactrum tritici Silenced for Arsenite Efflux Pumps.Sousa T, Branco R, Piedade AP, Morais PVPLoS One10.1371/journal.pone.01313172015Arsenic/*toxicity, Arsenite Transporting ATPases/deficiency/*genetics, Bacterial Proteins/*genetics/metabolism, Biodegradation, Environmental, Drug Resistance, Bacterial/genetics, Environmental Pollutants/*toxicity, *Gene Expression Regulation, Bacterial, Genetic Engineering, Ion Transport, *Mutation, Ochrobactrum/*drug effects/genetics/metabolism, OperonPathogenicity
Metabolism26735734Immobilization of Ochrobactrum tritici As5 on PTFE thin films for arsenite biofiltration.Branco R, Sousa T, Piedade AP, Morais PVChemosphere10.1016/j.chemosphere.2015.12.0252015Arsenites/*metabolism, Ochrobactrum/*metabolism, Polymers, Polytetrafluoroethylene/*metabolism, Waste Disposal, Fluid/*methods, Water Pollutants, Chemical/*metabolism
Metabolism31965334Arsenic accumulation by a rhizosphere bacterial strain Ochrobactrum tritici reduces rice plant arsenic levels.Moens M, Branco R, Morais PVWorld J Microbiol Biotechnol10.1007/s11274-020-2800-02020Arsenic/*analysis/toxicity, Biodegradation, Environmental, Crops, Agricultural/chemistry/growth & development/microbiology, Ochrobactrum/*growth & development/metabolism, Oryza/chemistry/growth & development/*microbiology, Plant Shoots/chemistry/growth & development/microbiology, Rhizosphere, Soil Pollutants/analysis/toxicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5003Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13340)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13340
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
23335M Lebuhn, W Achouak, M Schloter, O Berge, H Meier, M Barakat, A Hartmann, T Heulin10.1099/00207713-50-6-2207Taxonomic characterization of Ochrobactrum sp. isolates from soil samples and wheat roots, and description of Ochrobactrum tritici sp. nov. and Ochrobactrum grignonense sp. nov.IJSEM 50: 2207-2223 200011155998
33780Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4802
57511Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47104)https://www.ccug.se/strain?id=47104
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67772Curators of the UCCCBhttps://ucccb.uc.pt/
68369Automatically annotated from API 20NE
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
71528Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13104.1StrainInfo: A central database for resolving microbial strain identifiers